MolNFT v1 · #119924 · protein
Structure of the human 26S proteasome bound to USP14-ubal
5GJQ · Proteasome subunit beta type-6: “Structure of the human 26S proteasome bound to USP14-ubal”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #119924 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GJQ
- Type
- protein
- Length
- 13,520 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit beta type-6; Proteasome subunit alpha type-6; Proteasome subunit beta…
- EC
- 3.4.25.1, 3.4.19.-, 3.4.19.12
- UniProt
- P28072, P60900, Q99436, P25787, P49720, P25789, P49721, O14818, P28074, P28066, P20618, P25786, P28070, P35998, P62191, P62195, P43686, P62333, P17980, Q99460, P25788, Q9UNM6, O00232, O00231, Q15008, O43242, P48556, P51665, O00487, P55036, P60896, Q13200, P54578, P0CG47
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 36 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, o | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 202 | 35% helix, 29% strand | P28072 |
| B, h | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 244 | 36% helix, 25% strand | P60900 |
| b, p | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 30% helix, 32% strand | Q99436 |
| C | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 233 | 33% helix, 25% strand | P25787 |
| c, q | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 31% strand | P49720 |
| D, j | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 250 | 36% helix, 27% strand | P25789 |
| d, r | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 199 | 33% helix, 35% strand | P49721 |
| E, k | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 243 | 36% helix, 21% strand | O14818 |
| e, s | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 36% helix, 34% strand | P28074 |
| F, l | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 234 | 33% helix, 29% strand | P28066 |
| f, t | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 30% helix, 32% strand | P20618 |
| G, m | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 34% helix, 26% strand | P25786 |
| g | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 216 | 34% helix, 33% strand | P28070 |
| H | 26S protease regulatory subunit 7 | protein | 380 | 39% helix, 13% strand | P35998 |
| I | 26S protease regulatory subunit 4 | protein | 359 | 38% helix, 15% strand | P62191 |
| i | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 231 | 33% helix, 25% strand | P25787 |
| J | 26S protease regulatory subunit 8 | protein | 358 | 45% helix, 13% strand | P62195 |
| K | 26S protease regulatory subunit 6B | protein | 380 | 40% helix, 13% strand | P43686 |
| L | 26S protease regulatory subunit 10B | protein | 375 | 42% helix, 13% strand | P62333 |
| M | 26S protease regulatory subunit 6A | protein | 376 | 40% helix, 12% strand | P17980 |
| N | 26S proteasome non-ATPase regulatory subunit 1 | protein | 823 | 62% helix, 1% strand | Q99460 |
| n, X | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 243 | 35% helix, 26% strand | P25788 |
| O | 26S proteasome non-ATPase regulatory subunit 13 | protein | 372 | 68% helix, 4% strand | Q9UNM6 |
| P | 26S proteasome non-ATPase regulatory subunit 12 | protein | 413 | 72% helix, 3% strand | O00232 |
| Q | 26S proteasome non-ATPase regulatory subunit 11 | protein | 421 | 73% helix, 3% strand | O00231 |
| R | 26S proteasome non-ATPase regulatory subunit 6 | protein | 376 | 69% helix, 3% strand | Q15008 |
| S | 26S proteasome non-ATPase regulatory subunit 3 | protein | 395 | 71% helix, 3% strand | O43242 |
| T | 26S proteasome non-ATPase regulatory subunit 8 | protein | 258 | 65% helix, 3% strand | P48556 |
| U | 26S proteasome non-ATPase regulatory subunit 7 | protein | 283 | 48% helix, 18% strand | P51665 |
| u | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 217 | 33% helix, 33% strand | P28070 |
| V | 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) | protein | 257 | 45% helix, 18% strand | O00487 |
| W | 26S proteasome non-ATPase regulatory subunit 4 | protein | 193 | 39% helix, 17% strand | P55036 |
| Y | 26S proteasome complex subunit DSS1 | protein | 59 | 61% helix, 0% strand | P60896 |
| Z | 26S proteasome non-ATPase regulatory subunit 2 | protein | 732 | 51% helix, 1% strand | Q13200 |
| x | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 355 | 24% helix, 22% strand | P54578 |
| y | Polyubiquitin-B | protein | 76 | 20% helix, 30% strand | P0CG47 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains H, I, J, K, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.86 | 0.88 | 123 | ADP |
| 2 | 566 | 0.86 | 0.91 | 96 | empty |
| 3 | 994 | 0.83 | 0.84 | 137 | empty |
| 4 | 1139 | 0.83 | 0.84 | 119 | empty |
| 5 | 844 | 0.83 | 0.86 | 153 | empty |
Interfaces
162 interfaces between chains.
- L–M · 3837 Ų buried · 49 hydrogen bonds · protein-protein
- U–V · 3741 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 3199 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2970 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 2802 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide, 1 modified (isopeptide, nonstandard).
Compared structures
- P28070 · AlphaFold monomer V2.0 prediction for proteasome subunit beta type-4 (P28070) · a predicted model of the same protein · chain g against A, TM-score 0.99
- P25786 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-1 (P25786) · a predicted model of the same protein · chain G against A, TM-score 0.99
- P49720 · AlphaFold monomer V2.0 prediction for proteasome subunit beta type-3 (P49720) · a predicted model of the same protein · chain c against A, TM-score 0.99
- P49721 · AlphaFold monomer V2.0 prediction for proteasome subunit beta type-2 (P49721) · a predicted model of the same protein · chain d against A, TM-score 0.99
- Q99436 · AlphaFold monomer V2.0 prediction for proteasome subunit beta type-7 (Q99436) · a predicted model of the same protein · chain b against A, TM-score 0.99
- P25788 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-3 (P25788) · a predicted model of the same protein · chain n against A, TM-score 0.99
- P28066 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha type-5 (P28066) · a predicted model of the same protein · chain F against A, TM-score 0.97
- Q99460 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 1… · a predicted model of the same protein · chain N against A, TM-score 0.96
- P54578 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 14 (P54578) · a predicted model of the same protein · chain x against A, TM-score 0.96
- O00232 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 12… · a predicted model of the same protein · chain P against A, TM-score 0.95
- O43242 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 3… · a predicted model of the same protein · chain S against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P28072
- Every structure of UniProt P60900
- Every structure of UniProt Q99436
- Every structure of UniProt P25787
- Every structure of UniProt P49720
- Every structure of UniProt P25789
- Every structure of UniProt P49721
- Every structure of UniProt O14818
- Every structure of UniProt P28074
- Every structure of UniProt P28066
- Every structure of UniProt P20618
- Every structure of UniProt P25786
- Every structure of UniProt P28070
- Every structure of UniProt P35998
- Every structure of UniProt P62191
- Every structure of UniProt P62195
- Every structure of UniProt P43686
- Every structure of UniProt P62333
- Every structure of UniProt P17980
- Every structure of UniProt Q99460
- Every structure of UniProt P25788
- Every structure of UniProt Q9UNM6
- Every structure of UniProt O00232
- Every structure of UniProt O00231
- Every structure of UniProt Q15008
- Every structure of UniProt O43242
- Every structure of UniProt P48556
- Every structure of UniProt P51665
- Every structure of UniProt O00487
- Every structure of UniProt P55036
- Every structure of UniProt P60896
- Every structure of UniProt Q13200
- Every structure of UniProt P54578
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5GJQ · PDBe 5GJQ · UniProt P28072 · UniProt P60900 · UniProt Q99436 · UniProt P25787 · UniProt P49720 · UniProt P25789 · UniProt P49721 · UniProt O14818 · UniProt P28074 · UniProt P28066 · UniProt P20618 · UniProt P25786 · UniProt P28070 · UniProt P35998 · UniProt P62191 · UniProt P62195 · UniProt P43686 · UniProt P62333 · UniProt P17980 · UniProt Q99460 · UniProt P25788 · UniProt Q9UNM6 · UniProt O00232 · UniProt O00231 · UniProt Q15008 · UniProt O43242 · UniProt P48556 · UniProt P51665 · UniProt O00487 · UniProt P55036 · UniProt P60896 · UniProt Q13200 · UniProt P54578 · UniProt P0CG47
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